DUBAI (Reuters) - Al Qaeda leader Ayman al-Zawahri has told the Islamist militants who are some of Syria's toughest opposition forces to avoid alliances with other rebel fighters backed by Gulf Arab states and the West.

His comment reflects a deepening rift between groups of the Western- and Arab-backed Free Syrian Army (FSA) and guerrillas sympathetic to Zawahri's ultra hardline network, which seeks to wage a transnational armed campaign against the West.

Division among rebel fighters, as well as the influence of hardline Islamists, is one reason Western powers have hesitated to intervene in Syria's two-and-a-half-year-old conflict, in which more than 100,000 people have been killed.

In an audio speech released a day after the 12th anniversary of the 9/11 strikes, Zawahri said the United States would try to push opposition fighters to link up with "secular parties that are allied to the West", the SITE monitoring service said.

"I warn my brothers and people in the Syria of unity and jihad against coming close to any of these groups," he said. A full translation of Zawahri's remarks, containing the passage on Syria, was published by SITE on Sunday.

Zawahri's language makes clear he is referring to the FSA. Even though not all of the FSA's constituent groups are secular, its acceptance of support from the West and Gulf Arab monarchies renders it illegitimate in the eyes of al Qaeda.

Zawahri said events in Egypt supported his argument. He was referring to the July 3 removal of Islamist president Mohamed Mursi and the subsequent killing of hundreds of Islamists in a crackdown on the Muslim Brotherhood, a proponent of the representative democracy al Qaeda abhors.

Rivalries have been growing between the FSA and the Islamists, whose smaller but better trained and equipped forces control most of the rebel-held parts of northern Syria.

The two sides have fought together from time to time, but the FSA, desperate for greater firepower, has recently tried to distance itself to ease U.S. fears any arms it might supply could reach al Qaeda.

In July, al Qaeda-linked militants assassinated one of the top FSA commanders, Kamal Hamami, in a demonstration of just how damaged relations have become.

Zawahri, suspected by many security specialists to be living in the Pakistan-Afghanistan border area, denied what he said were assertions by the West that al Qaeda was guilty of indiscriminate attacks on markets and mosques in Syria.

"All who shed the forbidden blood of a Muslim or non-Muslim, we are innocent of this act, and if they are from us then we will seek to hold them accountable," he said.